rnaseq

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Is it possible to get exon counts without summarising over genes or transcripts? In addition, on [parameter reference](https://nf-co.re/rnaseq/3.8.1/parameters) webpage, the help for this parameter `--featurecounts_feature_type` might be wrong. It's probably...

royfrancis

Add new testing strategy based on nf-test files

2

Changes: - Workflow now parses repo for changed files with Python - Runs relevant tests by listing their nf-test files as the matrix of values - Uses tags to check...

adamrtalbot

Simple pipeline level nf-tests

1

The role of this PR is to open a discussion on how to organise and run pipeline level tests. I have directly replaced the existing tests with simple tests which...

adamrtalbot

[skip ci] Dev -> Master for 3.15.0

1

- Adds nf-test to all components of pipeline

drpatelh

Bumps bam_markduplicates_picard which was raising a linting error. ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a...

adamrtalbot

### Description of the bug A while ago we realized that `QUALIMAP` assigns more reads to exonic+intronic+intergenic than total reads in the sample. We subsampled the paired-end SRA FASTQ to...

ctuni

Fix genomeAttribute usage

1

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

maxulysse

Custom config being ignored

4

### Description of the bug - Custom config file: ``` process { withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR' { // single job memory = 80.GB cpus = 32 time = 4d }, withName: 'FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX'...

sklages

Improved ext.args consolidation for STAR and TRIMGALORE

3

Occasionally, people were surprised that parameters provided to `extra_star_align_args` could still conflict with the default configuration (e.g. #1046). As a convenience parameter, I felt that it should never take precedence...

MatthiasZepper

`NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (pituitary_stage3-1)` terminated with an error exit status (1)

4

### Description of the bug running rnaseq-pipeline locally and I'm having trouble with fail to read the header from "-". ### Command used and terminal output ```console # my cmd...

hyBio